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1. Xu, Yaomin. New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data.

Degree: PhD, Statistics, 2008, Case Western Reserve University School of Graduate Studies

Statistical data mining is one of the most active research areas. In this thesis we develop two new data mining procedures and explore their applications to genetic data. The first procedure is called PfCluster - Profile Cluster Analysis. It is a clustering method designed for profiled genetic data. The PfCluster is efficient and flexible in uncovering clusters determined by a new class of biologically meaningful distance metrics. A new internal quality measure of clusters, coherence index, is developed to find coherent clusters. An efficient mechanism for choosing the threshold of coherent clusters is also derived and implemented. The threshold is based on the first and second order approximations to the true threshold under a null distribution for parallel clusters. The PfCluster has been applied to simulated data and two real data examples: a biomarker LOH dataset and a microarray gene expression dataset. PfCluster is competitive to the correlation-based clustering procedures. The second procedure is called RPselection - Resampling based partitioning selection. It is a feature selection algorithm designed for microarray studies. It selects a subset of genes that maximizes a fitness score. The fitness score measures the relevance between the partition labels from a clustering result and an external class label derived from the clinical outcomes. The score is computed using a resampling procedure. The RPselection algorithm has been applied to simulated data and a real uveal melanoma gene expression data. RPselection outperforms gene-by-gene test-based feature selection procedures. Software development is an integral part of modern statistical research. Two software packages, pfclust and rpselect, are developed in this thesis based on our PfCluster method and RPselection algorithm. Packages pfclust and rpselect are implemented based on R object-oriented programming framework, and they can be easily customized and extended by users. The ideas in our two procedures can be generalized and applied to other data mining tasks. This thesis concludes with discussion on connections between two methods and the related future research. Advisors/Committee Members: Sun, Jiayang (Advisor).

Subjects/Keywords: Statistics; Bioinformatics; coherence index; data mining; feature selection; gene expression pathway; gene profiling; informative gene; microarray data; profile cluster analysis; partitioning; regulatory network; statistical pattern recognition

…profiling, informative gene, microarray data, profile cluster analysis, partitioning, regulatory… …folate acid data . . . . . . Gene expression profiles of top 0.1 % of genes in Folate data… …3.4 Probability that each gene is selected at least once in the RPselection algorithm… …Applications to Gene Microarray Data Abstract by Yaomin Xu Statistical data mining is one of the… …microarray gene expression dataset. PfCluster is competitive to the correlation-based clustering… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Xu, Y. (2008). New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data. (Doctoral Dissertation). Case Western Reserve University School of Graduate Studies. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=case1196144281

Chicago Manual of Style (16th Edition):

Xu, Yaomin. “New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data.” 2008. Doctoral Dissertation, Case Western Reserve University School of Graduate Studies. Accessed May 08, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case1196144281.

MLA Handbook (7th Edition):

Xu, Yaomin. “New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data.” 2008. Web. 08 May 2021.

Vancouver:

Xu Y. New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data. [Internet] [Doctoral dissertation]. Case Western Reserve University School of Graduate Studies; 2008. [cited 2021 May 08]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1196144281.

Council of Science Editors:

Xu Y. New Clustering and Feature Selection Procedures with Applications to Gene Microarray Data. [Doctoral Dissertation]. Case Western Reserve University School of Graduate Studies; 2008. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=case1196144281


Queens University

2. Clark, Nate. A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) .

Degree: Biology, Queens University

Our understanding of the mechanisms driving population divergence is dependent on our ability to effectively detect and interpret patterns of genetic differentiation. In natural populations, the evolutionary processes influencing genetic differentiation can be difficult to ascertain. Seabirds are highly mobile, yet often display population differentiation, suggesting intrinsic barriers to gene flow are important in driving their diversification. The northern gannet (Morus bassanus), a piscivorous, colonial seabird, is widely distributed across the North Atlantic Ocean. Despite strong dispersal abilities, decades of banding studies indicate that the North Atlantic Ocean acts as an effective barrier for migration in northern gannets. However, recent telemetry revealed that some northern gannets migrate across the ocean each year, suggesting trans-Atlantic gene flow is possible. To investigate population differentiation in northern gannets, I analyzed genomic patterns of diversity among eight North American and European colonies. Genetic structure was characterized using indices of genetic differentiation, principal component analysis, a Bayesian clustering method, and discriminant analysis of principal components. I found significant population genetic structure across the breeding range, corresponding primarily to the division between North American and European gannet populations. My analyses did not find significant differentiation among colonies on either side of the Atlantic. I employed Bayesian approaches to estimate contemporary gene flow and divergence between North American and European gannet populations. I found low but significant rates of migration from Europe into North America, but no migration from North America into Europe. My analyses suggest that North American and European populations diverged recently, potentially occupying separate refugia during the Last Glacial Maximum. Finally, I used outlier analysis and random forest feature selection to investigate fine-scale genetic structure, and identified loci that allowed population assignment of 85% of sampled northern gannets. Low genetic differentiation in northern gannets may be due to shared variation following recent range expansion or to admixture resulting from overlap in nonbreeding distribution. My results suggest that the North Atlantic Ocean acts as a semi-permeable barrier to gene flow in northern gannets. The informative genetic markers I identified may allow colony-specific impact assessment and the development of targeted management strategies in northern gannets.

Subjects/Keywords: Northern Gannet ; Morus Bassanus ; Outlier ; Random Forest ; Genetic Structure ; Genetic Differentiation ; ddRADseq ; Seabird ; Migration ; Gene Flow ; Divergence ; Refugium ; Genomics ; High-Throughput Sequencing ; Batch Effect ; Last Glacial Maximum ; Intrinsic Barriers ; Extrinsic Barriers ; Semi-Permeable Barrier ; Trans-Atlantic ; Fine-Scale Genetic Structure ; Conservation ; SNPs ; Informative Loci ; Population Assignment ; Randomization

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Clark, N. (n.d.). A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/23834

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Clark, Nate. “A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) .” Thesis, Queens University. Accessed May 08, 2021. http://hdl.handle.net/1974/23834.

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Clark, Nate. “A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) .” Web. 08 May 2021.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

Clark N. A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) . [Internet] [Thesis]. Queens University; [cited 2021 May 08]. Available from: http://hdl.handle.net/1974/23834.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Council of Science Editors:

Clark N. A 'Jaunt' Across the Pond: Investigating Patterns of Genetic Differentiation and Trans-Atlantic Migration in a Temperate Seabird (Morus Bassanus) . [Thesis]. Queens University; Available from: http://hdl.handle.net/1974/23834

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

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